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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ), 'gf_id' => 'HOM05D001339', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001339' ), 'data_identifier' => 'HOM05D001339', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001339', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '470', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p34660' => 'bna', 'A03p41520' => 'bna', 'A05p29120' => 'bna', 'A06p03170' => 'bna', 'A10p06490' => 'bna', 'Aa31LG10G3890' => 'aar', 'Aa31LG3G16250' => 'aar', 'Aa31LG8G6780' => 'aar', 'Aa31sc152G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.3406' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1809' => 'aag', 'Actinidia11644' => 'ach', 'Actinidia11646' => 'ach', 'Actinidia15340' => 'ach', 'Actinidia23141' => 'ach', 'Actinidia23820' => 'ach', 'Actinidia34517' => 'ach', 'Ah.08g217550' => 'amhyb', 'Ah.15g094750' => 'amhyb', 'AL1G20890' => 'aly', 'AL1G24210' => 'aly', 'AL1G24300' => 'aly', 'AL1G24420' => 'aly', 'AL1G26410' => 'aly', 'AL1G53420' => 'aly', 'AL1G58040' => 'aly', 'AL3G33650' => 'aly', 'AL6G21430' => 'aly', 'Aqoxy1G00060' => 'aox', 'Aqoxy3G02451' => 'aox', 'Aqoxy5G01597' => 'aox', 'Aqoxy6G00003' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3FZ8N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I28FP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5N4VNG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.78WJBV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.814T0F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8K57QZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FRF4XF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M6ATHE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ME03Z4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N4IWB8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQP7PG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TK8AAC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ULZ0R3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y21F8V' => 'arhy', 'AT1G47271' => 'ath', 'AT1G50400' => 'ath', 'AT3G20000' => 'ath', 'AT5G10860' => 'ath', 'ATR0068G112' => 'atr', 'ATR0568G077' => 'atr', 'ATR0796G115' => 'atr', 'Atru.chr10.2378' => 'acertr', 'Atru.chr10.2379' => 'acertr', 'Atru.chr10.2402' => 'acertr', 'Atru.chr12.1216' => 'acertr', 'Atru.chr13.449' => 'acertr', 'Atru.chr2.2534' => 'acertr', 'Atru.chr2.2541' => 'acertr', 'Atru.chr2.2572' => 'acertr', 'Atru.chr2.2573' => 'acertr', 'Atru.chr2.3728' => 'acertr', 'AUR62001375' => 'cqu', 'AUR62008631' => 'cqu', 'AUR62025591' => 'cqu', 'AUR62033140' => 'cqu', 'AUR62033854' => 'cqu', 'AUR62041669' => 'cqu', 'BcaB04g20672' => 'bca', 'BcaB06g26069' => 'bca', 'BcaB07g33845' => 'bca', 'BcaC01g03591' => 'bca', 'BcaC01g03592' => 'bca', 'BcaC03g13337' => 'bca', 'BcaC04g19279' => 'bca', 'BcaC05g28374' => 'bca', 'BcaC08g42940' => 'bca', 'BcaC09g48956' => 'bca', 'BolC1t04372H' => 'bol', 'BolC2t06430H' => 'bol', 'BolC3t17368H' => 'bol', 'BolC5t33176H' => 'bol', 'BolC6t35666H' => 'bol', 'BraA02t05056Z' => 'bra', 'BraA03t13306Z' => 'bra', 'BraA05t21795Z' => 'bra', 'BraA06t23528Z' => 'bra', 'C01p44090' => 'bna', 'C03p50840' => 'bna', 'C05p44520' => 'bna', 'C06p01840' => 'bna', 'C06p05590' => 'bna', 'CAN.G1226.34' => 'can', 'CAN.G1443.11' => 'can', 'CAN.G181.51' => 'can', 'CAN.G3.17' => 'can', 'CAN.G874.54' => 'can', 'CAN.G895.17' => 'can', 'CANSAT25G2476' => 'cansat', 'CANSAT54G1115' => 'cansat', 'CANSAT78G0076' => 'cansat', 'CARHR036830' => 'chi', 'CARHR040410' => 'chi', 'CARHR095530' => 'chi', 'CARHR202420' => 'chi', 'Carub.0001s1254' => 'cru', 'Carub.0001s3606' => 'cru', 'Carub.0001s3947' => 'cru', 'Carub.0003s1990' => 'cru', 'Carub.0006s0936' => 'cru', 'Ca_05734_v3' => 'car', 'Ca_15507_v3' => 'car', 'Ca_17248_v3' => 'car', 'CBR_g45690' => 'cbr', 'CBR_g57221' => 'cbr', 'Cc01_g15650' => 'ccan', 'Cc01_g15660' => 'ccan', 'Cc10_g02710' => 'ccan', 'CDE02G2561' => 'cde', 'CDE04G2801' => 'cde', 'CDE05G2195' => 'cde', 'CDE11G0548' => 'cde', 'Cfa008557' => 'cfa', 'Cfa018171' => 'cfa', 'Cfa018684' => 'cfa', 'Cfa024019' => 'cfa', 'Ciclev10003449m.g' => 'ccl', 'Ciclev10003909m.g' => 'ccl', 'Ciclev10032173m.g' => 'ccl', 'CiPaw.01G107500' => 'cil', 'CiPaw.02G058400' => 'cil', 'CiPaw.13G059200' => 'cil', 'CiPaw.14G047200' => 'cil', 'CiPaw.15G080500' => 'cil', 'CiPaw.16G059800' => 'cil', 'CiPaw.16G060000' => 'cil', 'ClCG02G018900' => 'cla', 'ClCG07G016660' => 'cla', 'ClCG08G014900' => 'cla', 'COL.COLO4_26293' => 'col', 'COL.COLO4_33124' => 'col', 'Cpa.g.sc247.4' => 'cpa', 'Cpa.g.sc70.24' => 'cpa', 'Cre10.g424450' => 'cre', 'CsaV3_2G028860' => 'csa', 'CsaV3_4G003790' => 'csa', 'CsaV3_6G013290' => 'csa', 'CSS0000014' => 'camsi', 'CSS0000778' => 'camsi', 'CSS0011393' => 'camsi', 'CSS0015861' => 'camsi', 'CSS0017435' => 'camsi', 'CSS0023381' => 'camsi', 'CSS0023896' => 'camsi', 'CSS0040771' => 'camsi', 'CSS0042877' => 'camsi', 'CSS0045685' => 'camsi', 'DCAR_017551' => 'dca', 'DCAR_018596' => 'dca', 'DCAR_018597' => 'dca', 'Dinv18269' => 'din', 'Dinv18270' => 'din', 'Dinv28769' => 'din', 'Dinv29695' => 'din', 'Dinv36097' => 'din', 'Dinv39432' => 'din', 'Duzib052G0423' => 'dzi', 'Duzib093G0419' => 'dzi', 'Duzib116G0938' => 'dzi', 'Duzib132G0334' => 'dzi', 'Duzib192G0625' => 'dzi', 'Duzib213G1068' => 'dzi', 'Duzib248G1082' => 'dzi', 'ECA232G0746' => 'eca', 'ECA236G4867' => 'eca', 'ECA246G0616' => 'eca', 'ECA247G0838' => 'eca', 'ECA247G3983' => 'eca', 'ECA248G2863' => 'eca', 'ECA248G3873' => 'eca', 'EL10Ac7g17508' => 'bvu', 'EL10Ac7g18232' => 'bvu', 'Eucgr.F01886' => 'egr', 'Eucgr.J00343' => 'egr', 'Eucgr.J03199' => 'egr', 'Eucgr.L01179' => 'egr', 'FAN07G0891' => 'fan', 'FAN11G1411' => 'fan', 'FAN12G0420' => 'fan', 'FAN12G3706' => 'fan', 'FAN15G2852' => 'fan', 'FAN16G0641' => 'fan', 'FAN17G0976' => 'fan', 'FAN20G1560' => 'fan', 'FAN21G3752' => 'fan', 'FAN22G1286' => 'fan', 'FAN25G0793' => 'fan', 'FAN27G1556' => 'fan', 'FvH4_2g39650' => 'fve', 'FvH4_3g41290' => 'fve', 'FvH4_4g11890' => 'fve', 'Glyma.02G238700' => 'gma', 'Glyma.04G031200' => 'gma', 'Glyma.05G241100' => 'gma', 'Glyma.06G031300' => 'gma', 'Glyma.08G048100' => 'gma', 'Glyma.14G207600' => 'gma', 'Gohir.A01G012100' => 'ghi', 'Gohir.A03G167500' => 'ghi', 'Gohir.A04G109448' => 'ghi', 'Gohir.A06G009500' => 'ghi', 'Gohir.A13G125200' => 'ghi', 'Gohir.D01G013300' => 'ghi', 'Gohir.D02G190600' => 'ghi', 'Gohir.D04G149200' => 'ghi', 'Gohir.D06G005000' => 'ghi', 'Gohir.D13G128900' => 'ghi', 'Gorai.002G015100' => 'gra', 'Gorai.005G213300' => 'gra', 'Gorai.010G009600' => 'gra', 'Gorai.012G135700' => 'gra', 'Gorai.013G145100' => 'gra', 'GSVIVG01009726001' => 'vvi', 'GSVIVG01024516001' => 'vvi', 'GSVIVG01038525001' => 'vvi', 'HanXRQChr01g0013431' => 'han', 'HanXRQChr01g0013691' => 'han', 'HanXRQChr05g0136431' => 'han', 'HanXRQChr08g0231021' => 'han', 'HanXRQChr08g0231041' => 'han', 'HanXRQChr09g0269041' => 'han', 'HanXRQChr11g0347311' => 'han', 'HanXRQChr12g0366321' => 'han', 'Haze_07069' => 'cav', 'Haze_07070' => 'cav', 'Haze_11068' => 'cav', 'Haze_17409' => 'cav', 'Haze_17944' => 'cav', 'Hma1.2p1_0161F.1_g071910' => 'hma', 'Hma1.2p1_0161F.1_g071920' => 'hma', 'Hma1.2p1_0203F.1_g086260' => 'hma', 'Hma1.2p1_0334F.1_g128420' => 'hma', 'Hma1.2p1_1631F.1_g294600' => 'hma', 'Hma1.2p1_1631F.1_g294620' => 'hma', 'HPP92_000810' => 'vpl', 'HPP92_011045' => 'vpl', 'HPP92_021162' => 'vpl', 'Hund05689' => 'sun', 'Hund18151' => 'sun', 'Hund18623' => 'sun', 'Hund26586' => 'sun', 'Lalb_Chr09g0330751' => 'lal', 'Lalb_Chr10g0103911' => 'lal', 'Lalb_Chr15g0085501' => 'lal', 'Lalb_Chr16g0387411' => 'lal', 'Lalb_Chr18g0053981' => 'lal', 'Lalb_Chr20g0117221' => 'lal', 'Lalb_Chr23g0266561' => 'lal', 'Lj1C108G11' => 'lonja', 'Lj1g0017478' => 'lja', 'Lj2A1108G29' => 'lonja', 'Lj2A1108T32' => 'lonja', 'Lj4A787G17' => 'lonja', 'Lj4g0016304' => 'lja', 'LjContig00141g0017332' => 'lja', 'Lsat_1_v5_gn_3_60440' => 'lsa', 'Lsat_1_v5_gn_4_117501' => 'lsa', 'Lsat_1_v5_gn_5_175961' => 'lsa', 'Lsat_1_v5_gn_7_45941' => 'lsa', 'Lsat_1_v5_gn_9_15561' => 'lsa', 'Lsat_1_v5_gn_9_15641' => 'lsa', 'Manes.02G210000' => 'mes', 'Manes.04G162300' => 'mes', 'Manes.11G000900' => 'mes', 'Manes.18G023300' => 'mes', 'Manes.18G121800' => 'mes', 'Mapoly0037s0137' => 'mpo', 'Mapoly0160s0023' => 'mpo', 'MBI10_g18262_MAGBIO' => 'mbi', 'MBI13_g00576_MAGBIO' => 'mbi', 'MBI18_g38874_MAGBIO' => 'mbi', 'MBI19_g37616_MAGBIO' => 'mbi', 'MCO01G796' => 'mco', 'MCO02G061' => 'mco', 'MCO02G350' => 'mco', 'MCO15G133' => 'mco', 'MD03G1045900' => 'mdo', 'MD04G1030900' => 'mdo', 'MD08G1030200' => 'mdo', 'MD11G1048200' => 'mdo', 'MD13G1002300' => 'mdo', 'MD13G1277300' => 'mdo', 'Medtr3g111940' => 'mtr', 'Medtr5g076080' => 'mtr', 'Medtr6g037360' => 'mtr', 'Medtr8g106010' => 'mtr', 'Medtr8g106050' => 'mtr', 'Medtr8g106070' => 'mtr', 'MELO3C010955.2' => 'cme', 'MELO3C017676.2' => 'cme', 'MELO3C019601.2' => 'cme', 'Migut.D00781' => 'egut', 'Migut.D00782' => 'egut', 'Migut.N00696' => 'egut', 'Migut.N00697' => 'egut', 'MSTRG.12726' => 'ama', 'MSTRG.12727' => 'ama', 'MSTRG.17940' => 'ama', 'MSTRG.17941' => 'ama', 'MSTRG.21286' => 'ama', 'Nitab4.5_0000539g0040' => 'nta', 'Nitab4.5_0000539g0050' => 'nta', 'Nitab4.5_0001759g0050' => 'nta', 'Nitab4.5_0002224g0160' => 'nta', 'Nitab4.5_0002641g0080' => 'nta', 'Nitab4.5_0003952g0030' => 'nta', 'Nitab4.5_0004383g0020' => 'nta', 'Nitab4.5_0004383g0060' => 'nta', 'Nn1g02868' => 'nnu', 'Nn1g09382' => 'nnu', 'Nn3g17513' => 'nnu', 'Nn4g23504' => 'nnu', 'Nn5g29642' => 'nnu', 'Nn7g37404' => 'nnu', 'Oeu020447.1' => 'oeu', 'Oeu023909.2' => 'oeu', 'Oeu034604.1' => 'oeu', 'Oeu037695.1' => 'oeu', 'Os01g0276200' => 'osa', 'Os01g0634900' => 'osa', 'Os03g0323800' => 'osa', 'Os03g0737000' => 'osa', 'Peaxi162Scf00020g01813' => 'pax', 'Peaxi162Scf00293g00041' => 'pax', 'Peaxi162Scf00293g00510' => 'pax', 'Peaxi162Scf00372g00719' => 'pax', 'PGR031G0902' => 'pgr', 'PGR044G2652' => 'pgr', 'PGR102G0880' => 'pgr', 'PGSC0003DMG400003738' => 'stu', 'PGSC0003DMG400020298' => 'stu', 'PGSC0003DMG402020176' => 'stu', 'Phvul.002G324200' => 'pvu', 'Phvul.008G243300' => 'pvu', 'Phvul.009G058600' => 'pvu', 'Potri.002G034800' => 'ptr', 'Potri.005G228300' => 'ptr', 'Potri.007G000200' => 'ptr', 'Potri.013G161500' => 'ptr', 'Potri.014G004100' => 'ptr', 'Potri.017G000100' => 'ptr', 'Pp3c16_22830' => 'ppa', 'Pp3c18_14610' => 'ppa', 'Pp3c22_19420' => 'ppa', 'Pp3c22_6740' => 'ppa', 'Pp3c25_12010' => 'ppa', 'Pp3c5_24660' => 'ppa', 'PRCOL_00000402' => 'pco', 'PRCOL_00005937' => 'pco', 'Prupe.1G180200' => 'ppe', 'Prupe.1G350100' => 'ppe', 'Prupe.1G377900' => 'ppe', 'Prupe.6G037200' => 'ppe', 'Psat2g048800' => 'psa', 'Psat5g012080' => 'psa', 'Psat7g004320' => 'psa', 'PSO170G0342' => 'pso', 'PSO339G6378' => 'pso', 'PSO357G0408' => 'pso', 'PSO384G4952' => 'pso', 'PSO407G0099' => 'pso', 'QL01p000742' => 'qlo', 'QL01p001417' => 'qlo', 'QL01p023409' => 'qlo', 'QL02p008982' => 'qlo', 'QL10p043911' => 'qlo', 'RcHm_v2.0_Chr4g0409321' => 'rch', 'RcHm_v2.0_Chr4g0447041' => 'rch', 'RcHm_v2.0_Chr5g0074091' => 'rch', 'RcHm_v2.0_Chr6g0301241' => 'rch', 'Rhsim01G0245800' => 'rsi', 'Rhsim06G0032000' => 'rsi', 'Rhsim13G0056400' => 'rsi', 'Sabra05G0176200' => 'sbr', 'Sabra07G0000200' => 'sbr', 'Sabra13G0129100' => 'sbr', 'Sabra14G0001700' => 'sbr', 'Sabra14G0004100' => 'sbr', 'SalBow2G0190' => 'sbo', 'SalBow6G3871' => 'sbo', 'SalBow7G3773' => 'sbo', 'Sc10g0009450' => 'sci', 'Sc15g0000900' => 'sci', 'Sc26g0003570' => 'sci', 'Sed0002329' => 'sed', 'Sed0005194' => 'sed', 'Sed0005884' => 'sed', 'Sed0008479' => 'sed', 'Sed0017810' => 'sed', 'SEGI_13312' => 'sgi', 'SEGI_26994' => 'sgi', 'SEGI_38927' => 'sgi', 'SGA_v2.0_scaffold120G33015' => 'sas', 'SGA_v2.0_scaffold1311G53909' => 'sas', 'SGA_v2.0_scaffold201G41410' => 'sas', 'SGA_v2.0_scaffold4G02314' => 'sas', 'SGA_v2.0_scaffold771G53579' => 'sas', 'SGA_v2.0_scaffold77G25332' => 'sas', 'SGA_v2.0_scaffold77G25334' => 'sas', 'SHI21181' => 'shi', 'SMO143G0004' => 'smo', 'SMO367G0551' => 'smo', 'Solyc04g080510.3' => 'sly', 'Solyc06g007710.4' => 'sly', 'Solyc06g082793.1' => 'sly', 'Solyc09g018750.3' => 'sly', 'Sopen04g034100' => 'spe', 'Sopen06g002600' => 'spe', 'Sopen06g034150' => 'spe', 'Sopen09g012290' => 'spe', 'Sp1g34410' => 'spa', 'Sp1g37220' => 'spa', 'Sp1g37230' => 'spa', 'Sp3g18030' => 'spa', 'Sp6g32610' => 'spa', 'TAR381G1655' => 'tar', 'TAR622G0423' => 'tar', 'TAR623G0286' => 'tar', 'TAR629G2379' => 'tar', 'THA.LOC104799019' => 'tha', 'THA.LOC104809025' => 'tha', 'THA.LOC104812559' => 'tha', 'THA.LOC104814988' => 'tha', 'THA.LOC104815250' => 'tha', 'THA.LOC104826511' => 'tha', 'Thecc.01G000200' => 'tca', 'Thecc.02G153700' => 'tca', 'Thecc.08G029000' => 'tca', 'Thecc.09G366900' => 'tca', 'Thhalv10011792m.g' => 'esa', 'Thhalv10012035m.g' => 'esa', 'Thhalv10014695m.g' => 'esa', 'Thhalv10021197m.g' => 'esa', 'TPR.G12403' => 'tpr', 'TPR.G15401' => 'tpr', 'TPR.G19258' => 'tpr', 'TWI31G1369' => 'twi', 'TWI36G0669' => 'twi', 'TWI53G0842' => 'twi', 'TWI74G0753' => 'twi', 'TWI77G0219' => 'twi', 'unitig_0.g2154' => 'ugi', 'unitig_22.g5199' => 'ugi', 'unitig_26.g10230' => 'ugi', 'unitig_6.g29276' => 'ugi', 'unitig_747.g21435' => 'ugi', 'vmacro02853' => 'vma', 'vmacro02854' => 'vma', 'vmacro14663' => 'vma', 'vmacro21651' => 'vma', 'VMungo0251G0670' => 'vmu', 'VMungo0647G2108' => 'vmu', 'VMungo1309G1079' => 'vmu', 'Zm00001eb015420' => 'zma', 'Zm00001eb056450' => 'zma', 'Zm00001eb128840' => 'zma', 'Zm00001eb169830' => 'zma', 'Zm00001eb332770' => 'zma', 'Zm00001eb395490' => 'zma' ) $gf_id = 'HOM05D001339' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001339' ) $data_identifier = 'HOM05D001339' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 2, 'aly' => (int) 9, 'aox' => (int) 4, 'arhy' => (int) 14, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 10, 'cqu' => (int) 6, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 4, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 7, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 7, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 5, 'hma' => (int) 6, 'vpl' => (int) 3, 'sun' => (int) 4, 'lal' => (int) 7, 'lonja' => (int) 4, 'lja' => (int) 3, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 5, 'nta' => (int) 8, 'nnu' => (int) 6, 'oeu' => (int) 4, 'osa' => (int) 4, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 2, 'ppe' => (int) 4, 'psa' => (int) 3, 'pso' => (int) 5, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 3, 'sbr' => (int) 5, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 7, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 6, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 3, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb395490' $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